Tuesday, August 28, 2007

Ive got two tests and a paper to worry about first tonight, but if you all are blissfully homework free: Go play!

So I woke up this morning, made some coffee, checked my e-mail, and did my usual Sitemeter/Technorati check. I had a ton of hits from UD. From a post on sea anemones. "Oh god" I thought "Theyre using my glowing viruses as Evidences for Intelligent Design(TM)."

Thankfully, that wasnt the case.

Someone just asked about my essay as a side comment (even Average Joe Creationists are uncomfortable with Behes silence). Sal was nice enough (silly enough?) to provide a link to my essay, happily removing all doubt that Behe is *unaware* of my post, and adding even more pressure on Behe to respond. LOL!

Anyway, I know 99% of you cant post at UD, so please feel free to leave comments here!

Response 1, 08-28-07:

Sal, thank you for providing me a forum where I can answer your questions.That makes you two steps ahead of Behe.To answer your questions—fine.Lets say all viruses in the lentivirus family related to HIV-1 lost their Vpu.It probably cropped up millions of years ago—long before we were there with Qiagen kits to watch what was happening, so I will happily entertain that possibility*.

HIV still does not have, quote, the ‘same number of genes.’If we grant your premise, all branches of immunodeficiency viruses ‘lost’ a gene.‘Same’ minus one.And, HIV-1 Vpu doesn’t look genetically or act biochemically like its ancestor, SIVcpz Vpu.They don’t ‘work in the same way.’Behe is still wrong.

Additionally, what has happened while we were watching is the evolution of the Subtype B and Subtype C sequences.Not only are HIV-1 Vpu sequences vastly different from SIVcpz Vpus, but B and C Vpus each have their own specific biochemical markers and specialties.We’ve watched that happen.Thus, Behe is still wrong.

And we have barely scratched the surface of HIV evolution.Hes only going to get ‘more wrong’ from here on out.

* We know Vpu is new in HIV-1 because of the directionality of necessity.As I referenced in my original essay, Vpu evolved in a very specific way in HIV-1 to overcome a cell specific and human specific host factor.Please see reference 10- I tried very hard to find PLoS/PubMedCentral references for this very purpose.

Response 2, 08-28-07:I believe Mike was referring specfically to human strains after the introduction into humans…

You dont want to reinterpret what Behe said this way. HIV-1 and HIV-2 are entirely different creatures. Also, HIV-2 has a gene duplication– something Behe said ’specifically’ hadnt happened in HIV.

He preferred to us directly observed evolutions rather than using interpretations possibly biased by a preconception such as a phylogeny…How, exactly, do you explain the apparent phylogeny of primate lentiviruses, then? And, this doesnt help your case. Again, lets grant your premise– HIV-1 is not related to SIVcpz. HIV-1 and HIV-2 are entirely different creatures. This makes things worse for Behe.

The Vpu protein did not emerge de novo after introduction into humans. Is that correct?Absolutely right, which I addressed in my essay: “Ah, Michael Behe, you might try to talk your way around Vpu now (though you were evidently unaware of its existence moments ago) by insisting that it is not *new* new.”

By the way, I appreciate your candor regarding the possibility of Vpu gene loss in ancient strains of HIV rather than gene emergence.Anything is a possibility with HIV. But experimental evidence is normally used to figure out which possibilities are viable, and which can be discarded. Vpu is a new gene, not a ‘lost in everyone else’ gene.

Response 3, 08-29-07: Davie has turned moderation on my comments so he can read them before everyone else. Im THAT exciting!

Sal-- *quip, sorry* HIV-1 is not AIDS. You progress to AIDS after being infected with HIV-1. :)

Again, I will grant your premise-- Behe meant nothing happened in HIV-1 AFTER it was introduced to humans.Behe still has a de novo multiprotein complex to worry about, and several de novo protein-protein interactions. He says that hasnt happened. He even made a table to say it hasnt happened.

I have never typed that Vpu is novel in humans. Its new in a branch of primate lentiviruses, again, look at reference 10. Its the sequence, biochemistry, and functionality that are different in humans.

Michael-- The number of phylogeny papers for HIV-1, 2, and SIV is massive (go to PubMed/PLos and search 'HIV phylogeny'). The easiest thing would be to point you towards the Los Alamos National Laboratory HIV sequence database. There, you can get sequences to line up yourself, if you dont believe anyone!

Dave-- Yup! Thats the quote (I knew he said it at least once)! HIV-2 has a new gene with lots of fun functions.Here is a recent (free) paper on the topic!

PaV-- Sure! HIV-1 could have gotten Vpu from the chimpanzee genome! The sequence is so divergent (not only in humans, but in SIVcpz) that we have no idea where it came from at this point. Its not an obvious gene duplication like Vpx.

But as I said in my essay and here-- HIV-1 Vpu and SIVcpz Vpu are totally different genetically, biochemically, and functionally. The main difference is that HIV-1 Vpus can form 'viroporins'. Thats pretty wild.The function they both have in common (destroying CD4 markers) is irreducibly complex in HIV-1... But not in SIVcpz. And then theres the evolution of novel protein binding/localization sequences in at least two subtypes (we havent looked at them all yet).

But the virus is still no more than a virus...*frown* There is a reason HIV-1 has taken over this planet while HIV-2 has not. Vpu is part of that reason.The differential evolution of Vpu between the subtypes points towards a way of stopping the subtype that is out competing every other HIV-1 out there.Youre free to believe Vpu evolution is 'insignificant', but I doubt HIV-1 would agree with you.

That is a very old Creationist Claim, btw.

Response 4, 8/29/07:

If we drive Ms. Smith away, others might think we had to resort to banning because we could not defend ourselves, or could not point out when her reading of Behe was inaccurate. This should be an easy thing to do, and no cause for getting rid of her.

Thank you, Sal. And your readers have brought up wonderful questions. However, answers will only be posted to questions on my blog if my comments are going to be ‘held in moderation’ here.

This is your blog– youre free to moderate as you see fit. But Im not wasting my time answering your readers questions if youre going to trash my responses.

Dave– Im looking at a copy of ‘Edge’ right now. Would you like to read it out loud together?“Yet through all that, there have been no significant biochemical changes in the virus at all…”

Response #5, 8/29/07:

Mike was referring to #1, and Ms. Smith to #2, therefore, because this is an equivocation, #2 cannot be used as a counter example to #1.

Vpu proteins interact with other Vpu proteins to create a tetramer-- a viroporin. Its also integral for particle release in humans, requiring more HIV protein-protein interactions. Completely new function/molecular machine in HIV-1. It is NOT in SIVcpz. And, Subtype C evolved biochemically to form these viroporins better than other subtypes. References for all of this is in my original essay.

Are you ready to start listing to what I say, or are you going to keep squirming?

28 comments:

Anonymous
said...

Hi Ms. Smith, I do hope you will visit the UD site. They opened up a new thread just for your case. I don't know if Behe will respond directly to you on the blog but many personal friends of his are there and it should be extremely interesting to watch a high level debate. Hopefully your homework will ease up to allow you to respond to them.

I note that already you have been warned by davescot; first and last apparently. What for is not entirely clear, although I think he is trying to suggest you are misrepresenting Behe on the subject of gene duplication.

This is simply bizzare, you don't ban someone right from the off like this, even if it is a genuine misrepresentation (and I'm not suggesting it is). Mad with power!

It's a shame the way davescot is behaving (you can add patronising to the list now), but I guess it's par for the course. I think your doing a pretty good job here and it shows Behe's research skills to be less than stellar.

However, one of the commenters does have a point; this is relatively tangential to Behe's main argument (malaria, mutations etc) which others have addressed. I actually tend to agree with Larry Moran that some of the reviews of Behe and his main argument have been rather poor. I'm looking forward to Larry's critique as I suspect it will take in what I think are the best ways to attack Behe; neutral mutations, plus I factor in epistasis and some of the recent literature on movement around evolutionary landscapes.

Also the latest stuff reconstructing actual mutational pathways; Behe's attempt to deal with the upcoming paper in Science (an attempt shredded by Jason Rosenhouse) was particularly feeble. I reckon it's this angle that can be used to go after Behe; demonstrating that he has a pretty naive and simplistic understanding of the evolutionary process and the way that mutations can work to create complex structures.

When your comment does show up, I bet they'll be all over you for using the term "creationist." In order to be taken seriously at UD, you're supposed to know (and agree with) their account of their intellectual history. The love between ID and creationism is a love that dare not speak its name (at least by critics).

This is exactly why it's a bad idea to try to engage the folks at UD. Sal set you up by pretending to want to listen and learn. But he doesn't, because (a) he already thinks he knows everything worth knowing, and (b) you're the enemy. Then he sends his army of idiots to drive you away by treating you like shit. Watch as he now claims victory because you have refused to play by his rules.

Hermagoras-- Oh I dont care if theyre 'mean'-- I think its endearing! Besides, there were lots of good questions on the thread. Really good ones! Ill probably answer them here in their own posts just so everyone can learn.

Once again, let me be perfectly clear-- I love questions. Im in the "there are no dumb questions" camp, whether youre a Creationist or a 'Darwinist'. I dont want anyone to be afraid theyll be ridiculed for asking a question.

But my comments will not be 'moderated'. I have better things to do than write posts to be deleted.

Sal, I do think is funny:Sal: "All other viruses could have LOST their Vpu!"Me: "Yes, thats a possibility. But the evidence doesnt point towards that direction. Heres a free online reference for you."Sal: "FRONT LOADING! FROOONT LOOOADING!"Me: "Nononono... We know which direction this went. That reference spells it out pretty well. Plus Vpu evolved new functions in humans..."Sal: "You know what I think is interesting? FRONT LOADING!!!"

UD is indeed following its established script - Cordova suggesting commenting and greasing up the commenter, and then Scot suggesting banning and establishing moderation. The final step to expect is to ban the commenter and claim victory in the UD thread.

Since everyone is busy watching ERV inject her wisdom into the senseless body of the UhD'uh site, I'm going to comment on Cordova's ingress.

Michael Behe has certainly given his critics a thrashing at his Amazon weblog.

When I saw Mike taking Ken Miller to task for Miller mischaracterizing Lipids as Proteins (a sophomoric mistake by Miller), I knew Mike was slamming the best the Darwinist could muster onto the floor.

This is of course the usual quote-mining of creationists, as Miller wouldn't make such a mistake. What Miller said was:

Telling his readers that the production of so much as a single new protein-to-protein binding site is “beyond the edge of evolution”, [Behe] proclaims darwinian evolution to be a hopeless failure. Apparently he has not followed recent studies exploring the evolution of hormone-receptor complexes by sequential mutations (Science 312, 97-101; 2006), the ‘evolvability’ of new functions in existing proteins — studies on serum paraxonase (PON1) traced the evolution of several new catalytic functions (Nature Genet. 37, 73-76; 2005) — or the modular evolution of cellular signalling circuitry (Annu. Rev. Biochem. 75, 655-680; 2006).

Miller lifted the discussion to general functional binding sites. What one could possibly say is that one wants example on Behe's p-p sites. Fine, the article by Arthur Hunt I linked to earlier give such examples, besides those discussed here.

Incidentally, Behe blocks comments on his Amazon site in the usual ID manner, so it is only a "weblog" in some tenuous creationist sense. The proper technical term for such behavior isn't "trashing", but "trash".

Your Behe takedown was fascinating stuff. Took several re-reads but I think I'm finally understanding it. One thing I'd like to see *someday* (I'm sure you are busy!) is a more graphic, simplified explanation of what is happening with the step-by step-HIV mutations.

Some thoughts on what I'd like to see included in such a thing, if it were ever done: the step by step relevant letter changes at the DNA sequence level, alongside the step by step changes in the amino acid sequences, alongside the 3D structural changes of Vpu itself ( with the changes in the binding sites marked), and a brief description of each change in function.

I know that would be some work, but I think it could be quite useful for explaining to people even less technical than I. Make the issues more accessible to a broader audience (like some of my fundie family members >:). How feasible is something like that?

Great effort at UD, but it's all very likely in vain. No amount of scientific evidence can sway our friend Sal Cordova.

Consider this factoid. As a YEC, he is holding out hope that geological and astronomical observations can somehow be reconciled with a 6,000-year-old Universe. Like maybe astronomical distances are smaller than they appear, the speed of light , binary stars aren't really binaries, the carbon dating method is wrong etc. etc. Sal's beyond redemption.

But by all means continue. It's fun to watch them going through contortions.

You've struck a nerve, to be sure. Anyways, the following was posted and then deleted last night on "your" UD thread. I thought I would add it to this discussion, just so the thoughts don't get permanently buried on my computer. And to prod you a bit about the TASK-1 paper.-------------------PaV, two points for now. First, the paper about TASK-1 is interesting. I'm not sure if HIV actually captured the N-terminus of TASK-1 as proposed by these authors. I have some ideas, but I'd rather give Abbie an opportunity to comment on this study. Regardless, this still leaves several (four? - I have to go back and count 'em) "CCC"'s that arose after the fact, as it were.

Second, you said: "Two things here: (1) what does the calculation look like wherein you arrive at these numbers; (2) in the case of T-urf-13, aren’t we dealing with: (a) mitochondrial plant DNA which, in the case of cms, is known to produce chimeric proteins, and (b) whose genetic mechanisms aren’t fully understood, and (c), in the case of ‘maize’, had to at some time been subjected to artificial selection, and therefore not a relevant comparison?"

The calculations I cite were posted by Ian Musgrave in the comments to Abbie's essay (these pertain to VPu) and by myself in the essay I linked to above. Points (a) (at least the part about chimeric proteins) and (b) you mention are not relevant to T-urf13.

Point c has never made much sense to me. (Think about it. What is more "natural" - parasite populations evolving as a consequence of exposure to a man-made chemical, or a breeder choosing a trait known to occur in nature, via random genetic variation? Put another way, I always get the feeling when someone says as you do that they believe that breeders in the 50's and 60's in some way designed T-urf13 from first principles and then went in and deliberately manipulated the maize mt genome to place the T-urf13 gene there. This is, to be honest, patently ludicrous. Of course, maybe you have something else in mind. Feel free to elaborate.)----------------------

No, I didn't save my posts. Silly me. I was careful to be polite so that I wouldn't get banned, didn't think it would be necessary. I'd heard they were fairly liberal with their banstick over there, but I really didn't expect to get banned.

The worst thing I said was that the guy who thought that there could be a family of viruses that existed for thousands of years in humans without leaving a single trace was describing a scenario that was possible, but fairly implausible.

Go figure...

I'll save my posts next time. Oh wait, I guess there won't be a next time...

Hey Factician - I tried to post this on yur blog, but didn't want to go through the bs of actually opening an account, so thanks for the bandwith Abbie...

You said:

The worst thing I said was that the guy who thought that there could be a family of viruses that existed for thousands of years in humans without leaving a single trace was describing a scenario that was possible, but fairly implausible.

Ha! That wasn't no Ordinary Guy! That was DaveScot Springer, the Guy with his pudgy finger on the Magic Bannanator Button!

For a complete history, complete with commentary, go to this link at ATBC:

But I hear they followed the ID script when Cordova's increasingly frantic attempts of trying to make it "not [ ] an appropriate counter example to Behe’s claims" became ridiculous and threatened to reveal Behe's empty claims on UD. (The final step to expect is to ban the commenter and claim victory in the UD thread.)

If you can't move the goalposts fast enough, remove the goal!

Btw, I note that Cordova managed to bare his ass on his fundamental ignorance of science on top of the discussed details. ("phylogenetic pre-conceptions" in place of predictions.)

As we all know, you don't have to do much to be banned on UD. All it takes is to show some knowledge in biology or other sciences. But since it is akin to poking a cesspit it merits a badge of honor.